When I press a key on my remote, the harmony hub flashes its led, so no battery or connectivity issue. 
RemoteBuddy is running on the mac, the BD remote is paired, and Plex HT is running (even set the Settings > System > Input Devices > Apple Remote to "Multi Remote (Harmony) and that isn't helping either.

It seems like Remote Buddy isn't recognizing any keypresses at all. 
Kind of at the end of my game here with configuring these two, I must say, if it's this hard to pair a simple remote to a simple keypress-forwarding scheme, it's not worth it switching to a remote in stead of the keyboard...